def __call__(self): MinimumResults = self.context.bika_setup.getMinimumResults() warning_icon = "<img " + \ "src='" + self.portal_url + "/++resource++bika.lims.images/warning.png' " + \ "height='9' width='9'/>" error_icon = "<img " + \ "src='" + self.portal_url + "/++resource++bika.lims.images/exclamation.png' " + \ "height='9' width='9'/>" header = _("Results per sample point") subheader = _( "Analysis results for per sample point and analysis service") self.contentFilter = {'portal_type': 'Analysis', 'review_state': ['verified', 'published']} parms = [] titles = [] val = self.selection_macros.parse_client(self.request) if val: self.contentFilter[val['contentFilter'][0]] = val['contentFilter'][1] parms.append(val['parms']) titles.append(val['titles']) val = self.selection_macros.parse_samplepoint(self.request) sp_uid = val if val: self.contentFilter[val['contentFilter'][0]] = val['contentFilter'][1] parms.append(val['parms']) titles.append(val['titles']) val = self.selection_macros.parse_sampletype(self.request) st_uid = val if val: self.contentFilter[val['contentFilter'][0]] = val['contentFilter'][1] parms.append(val['parms']) titles.append(val['titles']) val = self.selection_macros.parse_analysisservice(self.request) if val: self.contentFilter[val['contentFilter'][0]] = val['contentFilter'][1] parms.append(val['parms']) else: message = _("No analysis services were selected.") self.context.plone_utils.addPortalMessage(message, 'error') return self.default_template() val = self.selection_macros.parse_daterange(self.request, 'getDateSampled', 'DateSampled') if val: self.contentFilter[val['contentFilter'][0]] = val['contentFilter'][1] parms.append(val['parms']) titles.append(val['titles']) val = self.selection_macros.parse_state(self.request, 'bika_worksheetanalysis_workflow', 'worksheetanalysis_review_state', 'Worksheet state') if val: self.contentFilter[val['contentFilter'][0]] = val['contentFilter'][1] parms.append(val['parms']) # Query the catalog and store analysis data in a dict analyses = {} out_of_range_count = 0 in_shoulder_range_count = 0 analysis_count = 0 proxies = self.bika_analysis_catalog(self.contentFilter) if not proxies: message = _("No analyses matched your query") self.context.plone_utils.addPortalMessage(message, 'error') return self.default_template() # # Compile a list of dictionaries, with all relevant analysis data for analysis in proxies: analysis = analysis.getObject() result = analysis.getResult() client = analysis.aq_parent.aq_parent uid = analysis.UID() service = analysis.getService() keyword = service.getKeyword() service_title = "%s (%s)" % (service.Title(), keyword) result_in_range = self.ResultOutOfRange(analysis) if service_title not in analyses.keys(): analyses[service_title] = [] try: result = float(analysis.getResult()) except: # XXX Unfloatable analysis results should be indicated continue analyses[service_title].append({ 'service': service, 'obj': analysis, 'Request ID': analysis.aq_parent.getId(), 'Analyst': analysis.getAnalyst(), 'Result': result, 'Sampled': analysis.getDateSampled(), 'Captured': analysis.getResultCaptureDate(), 'Uncertainty': analysis.getUncertainty(), 'result_in_range': result_in_range, 'Unit': service.getUnit(), 'Keyword': keyword, 'icons': '', }) analysis_count += 1 keys = analyses.keys() keys.sort() parms += [ {"title": _("Total analyses"), "value": analysis_count}, ] ## This variable is output to the TAL self.report_data = { 'header': header, 'subheader': subheader, 'parms': parms, 'tables': [], 'footnotes': [], } plotscript = """ set terminal png transparent truecolor enhanced size 700,350 font "Verdana, 8" set title "%(title)s" set xlabel "%(xlabel)s" set ylabel "%(ylabel)s" set key off #set logscale set timefmt "%(date_format_long)s" set xdata time set format x "%(date_format_short)s\\n%(time_format)s" set xrange ["%(x_start)s":"%(x_end)s"] set auto fix set offsets graph 0, 0, 1, 1 set xtics border nomirror rotate by 90 font "Verdana, 5" offset 0,-3 set ytics nomirror f(x) = mean_y fit f(x) 'gpw_DATAFILE_gpw' u 1:3 via mean_y stddev_y = sqrt(FIT_WSSR / (FIT_NDF + 1)) plot mean_y-stddev_y with filledcurves y1=mean_y lt 1 lc rgb "#efefef",\ mean_y+stddev_y with filledcurves y1=mean_y lt 1 lc rgb "#efefef",\ mean_y with lines lc rgb '#ffffff' lw 3,\ "gpw_DATAFILE_gpw" using 1:3 title 'data' with points pt 7 ps 1 lc rgb '#0000ee' lw 2,\ '' using 1:3 smooth unique lc rgb '#aaaaaa' lw 2,\ '' using 1:4 with lines lc rgb '#000000' lw 1,\ '' using 1:5 with lines lc rgb '#000000' lw 1""" ## Compile plots and format data for display for service_title in keys: # used to calculate XY axis ranges result_values = [int(o['Result']) for o in analyses[service_title]] result_dates = [o['Sampled'] for o in analyses[service_title]] parms = [] plotdata = str() range_min = '' range_max = '' for a in analyses[service_title]: a['Sampled'] = a['Sampled'].strftime(self.date_format_long) if a[ 'Sampled'] else '' a['Captured'] = a['Captured'].strftime(self.date_format_long) if \ a['Captured'] else '' R = a['Result'] U = a['Uncertainty'] a['Result'] = a['obj'].getFormattedResult() in_range = a['result_in_range'] # result out of range if str(in_range[0]) == 'False': out_of_range_count += 1 a['Result'] = "%s %s" % (a['Result'], error_icon) # result almost out of range if str(in_range[0]) == '1': in_shoulder_range_count += 1 a['Result'] = "%s %s" % (a['Result'], warning_icon) spec = {} if hasattr(a["obj"], 'specification') and a["obj"].specification: spec = a["obj"].specification plotdata += "%s\t%s\t%s\t%s\t%s\n" % ( a['Sampled'], R, spec.get("min", ""), spec.get("max", ""), U and U or 0, ) plotdata.encode('utf-8') unit = analyses[service_title][0]['Unit'] if MinimumResults <= len(dict([(d, d) for d in result_dates])): _plotscript = str(plotscript) % { 'title': "", 'xlabel': t(_("Date Sampled")), 'ylabel': unit and unit or '', 'x_start': "%s" % min(result_dates).strftime( self.date_format_long), 'x_end': "%s" % max(result_dates).strftime( self.date_format_long), 'date_format_long': self.date_format_long, 'date_format_short': self.date_format_short, 'time_format': self.time_format, } plot_png = plot(str(plotdata), plotscript=str(_plotscript), usefifo=False) # Temporary PNG data file fh, data_fn = tempfile.mkstemp(suffix='.png') os.write(fh, plot_png) plot_url = data_fn self.request['to_remove'].append(data_fn) plot_url = data_fn else: plot_url = "" table = { 'title': "%s: %s" % ( t(_("Analysis Service")), service_title), 'parms': parms, 'columns': ['Request ID', 'Analyst', 'Result', 'Sampled', 'Captured'], 'data': analyses[service_title], 'plot_url': plot_url, } self.report_data['tables'].append(table) translate = self.context.translate ## footnotes if out_of_range_count: msgid = _("Analyses out of range") self.report_data['footnotes'].append( "%s %s" % (error_icon, t(msgid))) if in_shoulder_range_count: msgid = _("Analyses in error shoulder range") self.report_data['footnotes'].append( "%s %s" % (warning_icon, t(msgid))) self.report_data['parms'].append( {"title": _("Analyses out of range"), "value": out_of_range_count}) self.report_data['parms'].append( {"title": _("Analyses in error shoulder range"), "value": in_shoulder_range_count}) title = t(header) if titles: title += " (%s)" % " ".join(titles) return { 'report_title': title, 'report_data': self.template(), }
def __call__(self): MinimumResults = self.context.bika_setup.getMinimumResults() warning_icon = "<img " + \ "src='" + self.portal_url + "/++resource++bika.lims.images/warning.png' " + \ "height='9' width='9'/>" error_icon = "<img " + \ "src='" + self.portal_url + "/++resource++bika.lims.images/exclamation.png' " + \ "height='9' width='9'/>" header = _("Results per sample point") subheader = _( "Analysis results for per sample point and analysis service") self.contentFilter = { 'portal_type': 'Analysis', 'review_state': ['verified', 'published'] } parms = [] titles = [] val = self.selection_macros.parse_client(self.request) if val: self.contentFilter[val['contentFilter'] [0]] = val['contentFilter'][1] parms.append(val['parms']) titles.append(val['titles']) val = self.selection_macros.parse_samplepoint(self.request) sp_uid = val if val: self.contentFilter[val['contentFilter'] [0]] = val['contentFilter'][1] parms.append(val['parms']) titles.append(val['titles']) val = self.selection_macros.parse_sampletype(self.request) st_uid = val if val: self.contentFilter[val['contentFilter'] [0]] = val['contentFilter'][1] parms.append(val['parms']) titles.append(val['titles']) val = self.selection_macros.parse_analysisservice(self.request) if val: self.contentFilter[val['contentFilter'] [0]] = val['contentFilter'][1] parms.append(val['parms']) else: message = _("No analysis services were selected.") self.context.plone_utils.addPortalMessage(message, 'error') return self.default_template() val = self.selection_macros.parse_daterange(self.request, 'getDateSampled', 'DateSampled') if val: self.contentFilter[val['contentFilter'] [0]] = val['contentFilter'][1] parms.append(val['parms']) titles.append(val['titles']) val = self.selection_macros.parse_state( self.request, 'bika_worksheetanalysis_workflow', 'worksheetanalysis_review_state', 'Worksheet state') if val: self.contentFilter[val['contentFilter'] [0]] = val['contentFilter'][1] parms.append(val['parms']) # Query the catalog and store analysis data in a dict analyses = {} out_of_range_count = 0 in_shoulder_range_count = 0 analysis_count = 0 proxies = self.bika_analysis_catalog(self.contentFilter) if not proxies: message = _("No analyses matched your query") self.context.plone_utils.addPortalMessage(message, 'error') return self.default_template() # # Compile a list of dictionaries, with all relevant analysis data for analysis in proxies: analysis = analysis.getObject() result = analysis.getResult() client = analysis.aq_parent.aq_parent uid = analysis.UID() service = analysis.getService() keyword = service.getKeyword() service_title = "%s (%s)" % (service.Title(), keyword) result_in_range = self.ResultOutOfRange(analysis) if service_title not in analyses.keys(): analyses[service_title] = [] try: result = float(analysis.getResult()) except: # XXX Unfloatable analysis results should be indicated continue analyses[service_title].append({ 'service': service, 'obj': analysis, 'Request ID': analysis.aq_parent.getId(), 'Analyst': analysis.getAnalyst(), 'Result': result, 'Sampled': analysis.getDateSampled(), 'Captured': analysis.getResultCaptureDate(), 'Uncertainty': analysis.getUncertainty(), 'result_in_range': result_in_range, 'Unit': service.getUnit(), 'Keyword': keyword, 'icons': '', }) analysis_count += 1 keys = analyses.keys() keys.sort() parms += [ { "title": _("Total analyses"), "value": analysis_count }, ] ## This variable is output to the TAL self.report_data = { 'header': header, 'subheader': subheader, 'parms': parms, 'tables': [], 'footnotes': [], } plotscript = """ set terminal png transparent truecolor enhanced size 700,350 font "Verdana, 8" set title "%(title)s" set xlabel "%(xlabel)s" set ylabel "%(ylabel)s" set key off #set logscale set timefmt "%(date_format_long)s" set xdata time set format x "%(date_format_short)s\\n%(time_format)s" set xrange ["%(x_start)s":"%(x_end)s"] set auto fix set offsets graph 0, 0, 1, 1 set xtics border nomirror rotate by 90 font "Verdana, 5" offset 0,-3 set ytics nomirror f(x) = mean_y fit f(x) 'gpw_DATAFILE_gpw' u 1:3 via mean_y stddev_y = sqrt(FIT_WSSR / (FIT_NDF + 1)) plot mean_y-stddev_y with filledcurves y1=mean_y lt 1 lc rgb "#efefef",\ mean_y+stddev_y with filledcurves y1=mean_y lt 1 lc rgb "#efefef",\ mean_y with lines lc rgb '#ffffff' lw 3,\ "gpw_DATAFILE_gpw" using 1:3 title 'data' with points pt 7 ps 1 lc rgb '#0000ee' lw 2,\ '' using 1:3 smooth unique lc rgb '#aaaaaa' lw 2,\ '' using 1:4 with lines lc rgb '#000000' lw 1,\ '' using 1:5 with lines lc rgb '#000000' lw 1""" ## Compile plots and format data for display for service_title in keys: # used to calculate XY axis ranges result_values = [int(o['Result']) for o in analyses[service_title]] result_dates = [o['Sampled'] for o in analyses[service_title]] parms = [] plotdata = str() range_min = '' range_max = '' for a in analyses[service_title]: a['Sampled'] = a['Sampled'].strftime( self.date_format_long) if a['Sampled'] else '' a['Captured'] = a['Captured'].strftime(self.date_format_long) if \ a['Captured'] else '' R = a['Result'] U = a['Uncertainty'] a['Result'] = a['obj'].getFormattedResult() in_range = a['result_in_range'] # result out of range if str(in_range[0]) == 'False': out_of_range_count += 1 a['Result'] = "%s %s" % (a['Result'], error_icon) # result almost out of range if str(in_range[0]) == '1': in_shoulder_range_count += 1 a['Result'] = "%s %s" % (a['Result'], warning_icon) spec = {} if hasattr(a["obj"], 'specification') and a["obj"].specification: spec = a["obj"].specification plotdata += "%s\t%s\t%s\t%s\t%s\n" % ( a['Sampled'], R, spec.get("min", ""), spec.get("max", ""), U and U or 0, ) plotdata.encode('utf-8') unit = analyses[service_title][0]['Unit'] if MinimumResults <= len(dict([(d, d) for d in result_dates])): _plotscript = str(plotscript) % { 'title': "", 'xlabel': t(_("Date Sampled")), 'ylabel': unit and unit or '', 'x_start': "%s" % min(result_dates).strftime(self.date_format_long), 'x_end': "%s" % max(result_dates).strftime(self.date_format_long), 'date_format_long': self.date_format_long, 'date_format_short': self.date_format_short, 'time_format': self.time_format, } plot_png = plot(str(plotdata), plotscript=str(_plotscript), usefifo=False) # Temporary PNG data file fh, data_fn = tempfile.mkstemp(suffix='.png') os.write(fh, plot_png) plot_url = data_fn self.request['to_remove'].append(data_fn) plot_url = data_fn else: plot_url = "" table = { 'title': "%s: %s" % (t(_("Analysis Service")), service_title), 'parms': parms, 'columns': ['Request ID', 'Analyst', 'Result', 'Sampled', 'Captured'], 'data': analyses[service_title], 'plot_url': plot_url, } self.report_data['tables'].append(table) translate = self.context.translate ## footnotes if out_of_range_count: msgid = _("Analyses out of range") self.report_data['footnotes'].append("%s %s" % (error_icon, t(msgid))) if in_shoulder_range_count: msgid = _("Analyses in error shoulder range") self.report_data['footnotes'].append("%s %s" % (warning_icon, t(msgid))) self.report_data['parms'].append({ "title": _("Analyses out of range"), "value": out_of_range_count }) self.report_data['parms'].append({ "title": _("Analyses in error shoulder range"), "value": in_shoulder_range_count }) title = t(header) if titles: title += " (%s)" % " ".join(titles) return { 'report_title': title, 'report_data': self.template(), }
def __call__(self): header = _("Reference analysis QC") subheader = _("Reference analysis quality control graphs ") MinimumResults = self.context.bika_setup.getMinimumResults() warning_icon = "<img src='" + self.portal_url + "/++resource++bika.lims.images/warning.png' height='9' width='9'/>" error_icon = "<img src='" + self.portal_url + "/++resource++bika.lims.images/exclamation.png' height='9' width='9'/>" self.parms = [] titles = [] sample_uid = self.request.form.get('ReferenceSampleUID', '') sample = self.reference_catalog.lookupObject(sample_uid) if not sample: message = _("No reference sample was selected.") self.context.plone_utils.addPortalMessage(message, 'error') return self.default_template() self.parms.append( {'title': _("Reference Sample"), 'value': sample.Title()}) titles.append(sample.Title()) service_uid = self.request.form.get('ReferenceServiceUID', '') service = self.reference_catalog.lookupObject(service_uid) if not service: message = _("No analysis services were selected.") self.context.plone_utils.addPortalMessage(message, 'error') return self.default_template() self.contentFilter = {'portal_type': 'ReferenceAnalysis', 'review_state': ['verified', 'published'], 'path': { "query": "/".join(sample.getPhysicalPath()), "level": 0}} self.parms.append( {'title': _("Analysis Service"), 'value': service.Title()}) titles.append(service.Title()) val = self.selection_macros.parse_daterange(self.request, 'getDateVerified', 'DateVerified') if val: self.contentFilter[val['contentFilter'][0]] = val['contentFilter'][1] self.parms.append(val['parms']) titles.append(val['titles']) proxies = self.bika_analysis_catalog(self.contentFilter) if not proxies: message = _("No analyses matched your query") self.context.plone_utils.addPortalMessage(message, 'error') return self.default_template() # Compile a list with all relevant analysis data analyses = [] out_of_range_count = 0 results = [] capture_dates = [] plotdata = "" tabledata = [] for analysis in proxies: analysis = analysis.getObject() service = analysis.getService() resultsrange = \ [x for x in sample.getReferenceResults() if x['uid'] == service_uid][ 0] try: result = float(analysis.getResult()) results.append(result) except: result = analysis.getResult() capture_dates.append(analysis.getResultCaptureDate()) if result < float(resultsrange['min']) or result > float( resultsrange['max']): out_of_range_count += 1 try: precision = str(analysis.getPrecision()) except: precision = "2" try: formatted_result = str("%." + precision + "f") % result except: formatted_result = result tabledata.append({_("Analysis"): analysis.getId(), _("Result"): formatted_result, _("Analyst"): analysis.getAnalyst(), _( "Captured"): analysis.getResultCaptureDate().strftime( self.date_format_long)}) plotdata += "%s\t%s\t%s\t%s\n" % ( analysis.getResultCaptureDate().strftime(self.date_format_long), result, resultsrange['min'], resultsrange['max'] ) plotdata.encode('utf-8') result_values = [int(r) for r in results] result_dates = [c for c in capture_dates] self.parms += [ {"title": _("Total analyses"), "value": len(proxies)}, ] # # This variable is output to the TAL self.report_data = { 'header': header, 'subheader': subheader, 'parms': self.parms, 'tables': [], 'footnotes': [], } if MinimumResults <= len(proxies): plotscript = """ set terminal png transparent truecolor enhanced size 700,350 font "Verdana, 8" set title "%(title)s" set xlabel "%(xlabel)s" set ylabel "%(ylabel)s" set key off #set logscale set timefmt "%(timefmt)s" set xdata time set format x "%(xformat)s" set xrange ["%(x_start)s":"%(x_end)s"] set auto fix set offsets graph 0, 0, 1, 1 set xtics border nomirror rotate by 90 font "Verdana, 5" offset 0,-3 set ytics nomirror f(x) = mean_y fit f(x) 'gpw_DATAFILE_gpw' u 1:3 via mean_y stddev_y = sqrt(FIT_WSSR / (FIT_NDF + 1)) plot mean_y-stddev_y with filledcurves y1=mean_y lt 1 lc rgb "#efefef",\ mean_y+stddev_y with filledcurves y1=mean_y lt 1 lc rgb "#efefef",\ mean_y with lines lc rgb '#ffffff' lw 3,\ "gpw_DATAFILE_gpw" using 1:3 title 'data' with points pt 7 ps 1 lc rgb '#0000ee' lw 2,\ '' using 1:3 smooth unique lc rgb '#aaaaaa' lw 2,\ '' using 1:4 with lines lc rgb '#000000' lw 1,\ '' using 1:5 with lines lc rgb '#000000' lw 1""" % \ { 'title': "", 'xlabel': "", 'ylabel': service.getUnit(), 'x_start': "%s" % min(result_dates).strftime( self.date_format_short), 'x_end': "%s" % max(result_dates).strftime( self.date_format_short), 'timefmt': r'%Y-%m-%d %H:%M', 'xformat': '%%Y-%%m-%%d\n%%H:%%M', } plot_png = plot(str(plotdata), plotscript=str(plotscript), usefifo=False) # Temporary PNG data file fh, data_fn = tempfile.mkstemp(suffix='.png') os.write(fh, plot_png) plot_url = data_fn self.request['to_remove'].append(data_fn) plot_url = data_fn else: plot_url = "" table = { 'title': "%s: %s (%s)" % ( t(_("Analysis Service")), service.Title(), service.getKeyword() ), 'columns': [_('Analysis'), _('Result'), _('Analyst'), _('Captured')], 'parms': [], 'data': tabledata, 'plot_url': plot_url, } self.report_data['tables'].append(table) translate = self.context.translate ## footnotes if out_of_range_count: msgid = _("Analyses out of range") self.report_data['footnotes'].append( "%s %s" % (error_icon, t(msgid))) self.report_data['parms'].append( {"title": _("Analyses out of range"), "value": out_of_range_count}) title = t(header) if titles: title += " (%s)" % " ".join(titles) return { 'report_title': title, 'report_data': self.template(), }